SMTL ID : 4fdv.1

CobH from Rhodobacter capsulatus (SB1003) in complex with HBA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

2 x 0UK: 3-[(1R,2R,3R,5R,6S,7R,9Z,12S,13S,14Z,17S,18S,19R)-2,13,18-tris(2-hydroxy-2-oxoethyl)-3,12,17-tris(3-hydroxy-3-oxopropyl)-3,5,8,8,13,15,18,19-octamethyl-1,2,5,6,7,12,17,22-octahydrocorrin-7-yl]propanoic acid(Non-covalent)

0UK.1: 31 residues within 4Å: Chain A: G.9, I.12, Y.13, S.16, R.39, H.42, A.43, G.83, T.85, A.195, V.198, A.199, N.202 Chain B: A.77, R.78, M.79, L.99, Q.100, T.114, R.115, S.116, N.136, A.137, P.138, T.139, V.164, G.165, F.166, I.167, G.193, S.194 36 PLIP interactions: 22 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:T.114, B:A.137, A:I.12, A:Y.13, A:Y.13, A:A.43, A:A.195, A:V.198 Hydrogen bonds: B:R.78, B:M.79, B:Q.100, B:R.115, B:S.116, B:N.136, B:T.139, B:T.139, B:F.166, B:I.167, B:S.194, A:S.16, A:T.85 Water bridges: B:R.115, B:R.115, B:R.115, B:R.115, B:G.192, B:A.195, B:A.195, A:R.39, A:H.42, A:A.43, A:T.85 Salt bridges: B:R.115, B:R.115, A:R.39, A:H.42 0UK.4: 31 residues within 4Å: Chain A: A.77, R.78, M.79, L.99, Q.100, T.114, R.115, S.116, N.136, A.137, P.138, T.139, V.164, G.165, F.166, I.167, G.193, S.194 Chain B: G.9, I.12, Y.13, S.16, R.39, H.42, A.43, G.83, T.85, A.195, V.198, A.199, N.202 37 PLIP interactions: 15 interactions with chain B, 22 interactions with chain A Hydrophobic interactions: B:I.12, B:Y.13, B:Y.13, B:A.43, B:A.195, B:V.198, A:T.114, A:A.137 Hydrogen bonds: B:Y.13, B:S.16, B:T.85, A:R.78, A:M.79, A:Q.100, A:R.115, A:S.116, A:N.136, A:T.139, A:T.139, A:F.166, A:I.167, A:S.194 Water bridges: B:R.39, B:R.39, B:H.42, B:A.43, A:R.115, A:R.115, A:R.115, A:R.115, A:G.192, A:A.195, A:A.195 Salt bridges: B:R.39, B:H.42, A:R.115, A:R.115

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: H.143, N.146 Chain B: Y.5, K.7 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.5, B:K.7, B:K.7, A:H.143, A:N.146 Water bridges: A:N.113 GOL.3: 4 residues within 4Å: Chain A: R.155, P.181, V.182, P.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.155 GOL.5: 4 residues within 4Å: Chain A: Y.5, K.7 Chain B: H.143, N.146 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.143, B:N.146, A:K.7, A:K.7 Water bridges: B:N.113 GOL.6: 4 residues within 4Å: Chain B: R.155, P.181, V.182, P.183 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deery, E. et al., An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis. Nat.Chem.Biol. (2012)

Release Date

2012-10-17

Peptides

Precorrin-8X methylmutase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Precorrin-8X methylmutase